Hooded in Red
by AlessNox
Summary: Sherlock is dead, but he isn't really. Molly Hooper is the only one of his old friends to still be in contact with him in hiding. The only link back to his old life, and now that link is in danger of being cut. A story based on the tale of Little Red Riding Hood written for the Let's Write Sherlock: Challenge 2 on Tumblr and AO3
1. A visit to Grandmum

There was a crime wave in the city of London. Robberies, car thefts, even murders were on the rise. It seemed as if all Hell had broken loose since Sherlock Holmes had died. Most people didn't connect the two, but DI Lestrade did. His unsolved case files were almost as large now as his solved ones. Lestrade could honestly say that he missed Sherlock. He knew that he wasn't a fake, even though he saw the articles and the pictures in the paper calling him a trickster, a magician, a Svengali, and accusing him of fooling people, even Scotland Yard, into believing that he could solve crimes.

Scotland Yard had been criticized for falling for a charlatan, and Lestrade had felt the heat of that attention. His superior officers had reprimanded him, and he had been lucky to have survived with his job much less his rank. But the problem with Sherlock being dead was that his work was that much harder now that he wasn't around to help speed things along.

It had been a tiring day. DI Lestrade was in the market to buy a few things for dinner when he ran directly into Molly Hooper knocking both of their baskets to the ground.

"Oh sorry," Molly said bending down to pick up her things which had been mixed with his.

"Molly?" he said.

She turned to look up at him, her elbow just brushing the edge of his tan mackintosh. "Greg, I didn't expect to see you here?" Molly said.

"Well, It's good to see ya, Molly. It's been a long time."

"You've cut your hair."

"Yeah," he said running his fingers through the cropped silver-grey strands. He reached out to take a pair of frozen dinners placing them back into his basket before helping her to her feet.

Molly clasped her basket close to her sweater which was red and covered with little pink roses "I was just...how are you?" she said nervously.

"Fine," he said, "and you?"

"Fine," she said.

For a moment they simply stood saying nothing. Then Molly asked, "So, how has your work been?"

Lestrade sucked in a breath. "It's been challenging, frustrating really. We've been overrun with cases lately. It's like everyone's gone a little crazy. Arson, kidnapping, theft, most of the cases are easily solvable, but some aren't. I wish..." but he didn't finish the sentence. Both of knew that he was wishing that Sherlock was still around to help, but he wasn't, so Lestrade didn't bother to say it.

"It's lucky that I ran into you," Lestrade said, "because there were some questions that I wanted to ask you about certain types of wounds. I have this case. They look like they were made by a metal rod, but I'm not so sure. I used to ask Sherlock about these sorts of things but...anyway I was wondering if I could get your number for when I have questions that is, if you don't mind." Molly was silent. She looked toward the checkout counter. "Or if you prefer, I can give you my number and you can call me when you have time. Have you taken up smoking?"

"What?" Molly asked looking up to find his dark eyes staring at her.

"It's just that you have nicotine patches in your basket."

Molly flushed red. "Oh they're not for me," she said. "I'm going to meet my grandmother tonight and she uses them."

"Your grandmother?" Lestrade said. "Is she a smoker? The patches aren't very good for old skin I hear. They can cause damage."

"Oh, Grandmum's too set in her ways to stop now," Molly said. "I promised to drive out and give them too her tonight, so sorry, but I have to go now. Goodbye Greg," Molly said striding toward the check out.

"I was just leaving too," he said following her. He stood behind her in the queue. She looked at the door, at the ceiling, anywhere but his eyes. "So you'll be driving around alone tonight?" Lestrade said, "You should be careful. There's been lots of crime lately. The commissioner has issued a voluntary curfew. If you have to be out late, then you need to watch yourself."

Molly smiled, "I'm a grown woman. What could to happen to me? I'll be in my car? "

"Hopefully nothing bad will happen," he said. "Even so, I suggest that you go straight there and then go straight home. The streets of London are no place for a woman to be alone these days."

Molly grinned, "You sound like my dad. He was always afraid that something bad would happen to me, but it never has."

"I'm glad to hear it," Lestrade said. "Even so, heed my warning. Don't be out alone at night. Go there and back without stopping."

"Oh, alright," Molly said as she reached the checkout and began to unload the cans of beans, bread, milk, rubbing alcohol and instant coffee. "I'll be careful as I drive through the dark city at night." She said smiling as she paid for the items. Then she waved goodbye taking her bags and rushing out of the store. Lestrade bought his items and was walking toward the door before remembering that he had forgotten to give her his phone number.

* * *

Molly climbed into her little blue mini and started the engine. Both of Molly's grandmums were dead and had been for years. She pulled out into the street and started driving toward the some of the darkest grayest streets in the city. The very kind of places that Lestrade had warned her against.

The problem with Sherlock Holmes being dead in Molly Hooper's opinion, was that for a dead man he certainly needed a lot of stuff. She glanced over at her shopping bags to discover that other than a bag of cat food and some bottled water, everything else was for Sherlock. Looking at the clock on her phone, she realized that she had better rush if she wanted to get these supplies out to him and be back in time to watch her favorite shows on the telly.

She hadn't expected to see Greg Lestrade. Molly was always nervous when she was around people who had known Sherlock. She had never been a good liar, and she felt that somehow they would look at her and realize that she was lying about Sherlock's death. Sherlock had grilled it into her that absolutely no one must know, and she had been careful. But when someone told her straight out that they needed him, It was hard for her to stay silent.

She got off of the highway and wound through a series of streets finally pulling into a dark alley next to a broken streetlight. She turned off the engine and waited. The knock at her window startled her even though she was expecting it. Molly rolled down the window and saw Joe.

Joe had grey hair and an unruly grey beard. He looked very old, but Molly could tell by his hands that he was no more than forty. It was one of the perks of dealing with bodies all day. "Spare some change miss?" he asked. She looked around suspiciously to make sure that she hadn't been followed, then she passed out the bags of groceries. Afterwards, she handed him his payment. A tin of roasted cashews, and a large bag of gourmet jelly babies.

"There's milk in that," she said to remind him not to dawdle.

"Thank you miss, you are so generous," The man said reaching out to shake her hand. He passed her a note before turning and walking away.

Molly lay the note on her lap and unfolded it. It said '**2 dozen **_**Helianthus annuus**__**. **_**tonight.'**_Helianthus_ was the name for sunflowers. Where was she going to get sunflowers at this time of night? She turned to talk to Joe again, but he was gone.

Pulling out of the alley, she drove slowly through the streets without really noticing where she was going. Why was she like this? Why did Molly always feel compelled to give Sherlock whatever he wanted? He had always asked for things, from her, and she had not denied him, even when she should. She had even given him a complete human head once, and he had taken it without even a thank you. Turning the corner beside a row of shops, she drove slowly along the street looking for a florist. Why was she going out of her way to honor his strange request? What did he need sunflowers for anyway? Certainly flowers could wait until morning, but the note had said tonight, so...

She spotted a flower shop, and she pulled up to it. She stepped out of the car and walked over to the door to find it locked. Sighing loudly, she considering driving around aimlessly again, then she turned back and pounded on the door in case someone was inside. The lights were on, but no one answered. It was after curfew. The shops had probably decided that it wasn't worth staying open late.

As she turned toward to her car, she noticed a man on the sidewalk staring at her. She hadn't seen him before. It was as if he had appeared by magic. He was wearing a red hoodie and he stood very still with his hands in his pockets.

Molly looked around, but the rest of the street was deserted. They were the only two people visible on the entire block. "Hello," Molly said.

"Lookin' for flower's miss?" the man asked lifting his hands to pull down his hood. He was a young man with high cheekbones and raven black hair. His eyes glowed golden in the lamplight.

"Um, yes," Molly said, "For my grandmother. It's her birthday. I left it a bit late, but I'd really like to get some tonight. You don't know of someplace that sells flowers that is still open, do you?"

"I think that I do," The man said his hands back in his pockets. He stared back at her. His face was without a smile. "What kind of flowers did you need exactly, miss?"

"Sunflowers," she said.

"There are a number of places. It might help me if I knew more about where you were going. Where does your grandmother live?"

"Near the river, about three miles that way. Do you know of any places along the way."

"From here to the river? No." the man said, "But I do know of a twenty four hour flower market that will have sunflowers and whatever else that you need. It's a bit out of your way, but you could get it tonight."

"Can you give me the address to the flower shop?" Molly asked.

"Of course," the man said writing on a scrap of paper and passing it to her.

"Thanks!" she said climbing into the car and driving off. When she looked in the rearview mirror, the man was gone.

The store was everything that the man had said it was. It was fabulous. She had spent much more time there than she had expected to, so that it was near midnight by the time that she got to the factory. That's what she called the place where Sherlock was staying now. The building was situated on a lesser used street. It abutted the river. Once it had been a textile mill. Then it had been converted into flats, but the building had been condemned long ago.

She drove into the drive closing the gate behind her. She pulled out her phone to check the time, but the screen went dark immediately so she plugged it into the charger and tossed it onto the seat.

The side door was unlocked. It swung open silently letting her into the old style ivory painted kitchen. She turned on the light, and saw the bags of groceries that she had bought laid out on the table. The milk was sitting out, so she picked it up and put it in the nearby refrigerator. "Sherlock!" she called, "Sherlock!" but no one answered.

She placed the flowers on the table and walked into the hallway. Darkness stretched out to her right where the closed doors of a dozen abandoned rooms stood. She had always found this place a bit creepy. It was too big and too empty, so she crossed the hall quickly pushing her way into what once been a recreation room. Assorted tables stood abandoned in the middle of the room. Chairs were stacked against the wall beside a torn poster advertising vacation trips to Italy. A broken chair lay flat in the middle of the floor. The room was dark. The only illumination came from a small lamp on a table on the far side of the room. Silhouetted against the light was a dark haired man in a long black coat.

"Sherlock," Molly said rushing across the room. Her footsteps ringing off of the walls and ceiling. He did not turn. "Sherlock, why didn't you answer me? I brought your groceries. You need to eat more. Are you losing weight again? That coat is hanging off of your bones." She stood behind him, but he still faced away from her. "I brought you the flowers that you asked for." She said waiting for him to say something, to acknowledge her presence, but he just stood there. He seemed so still. "Are you all right?" Molly asked.

The man stood a bit taller before turning to face her. He was wearing a paper mask and on the mask was the image of Sherlock's face.

Molly slowly started to back away. Then the man placed a hand on the mask and she froze. Fear and curiosity holding her in place. He removed the mask to reveal high cheekbones and golden eyes. It was the man that she had seen on the street. The man in the red hoody. "Who are you?" Molly asked, "and where is Sherlock?"

"That's funny," the man said, " '_Where is Sherlock'_ is exactly the question that I was going to ask you Miss Molly Hooper."

Molly's mouth fell open as she stared into the man's unsmiling face. She turned, and began to run across the room only to find strong hands grabbing her shoulders and pulling her back. She saw the silver glint of a knife right before she felt the sharp blade against the skin of her neck. She looked up into those golden eyes, felt his breath against her shoulder as his lips finally did open up into a smile.

"Since the two of us are going to have a little chat, I suppose that introductions are in order. You of course are Molly Hooper. They call me The Engineer."


	2. The Wolf

Plastic twine dug into Molly's wrists and ankles. She was propped in one of the metal chairs in the rec room near a stack of discarded tables. "What do you want from me?" Molly asked.

"Nothing yet," the Engineer said. "I'll tell you when I need something." He was moving furniture around. He would shift the position of the table or the lamp every so often, then he would stand back and move them again.

"What are you doing?" Molly asked.

"Setting the stage," he said, "I've been waiting for this chance for quite a while."

"How did you find this place?" she asked, "I saw the groceries. Did you followed Joe to get here?"

"Eventually," he said, "he had run off, but I found him again using your directions. Didn't your parents ever tell you that you shouldn't talk to strangers?"

Molly frowned, tugging at her cords. They were no looser than before. "So where is Joe now?"

"Right there," he said hooking his thumb to the right. Molly turned and looked over her shoulder further into the darkened room. What she had taken for a rolled up bit of carpet was really a body, Joe's body. His mouth was hanging open, and his vacant eyes stared out at nothing. Molly screamed.

The engineer rushed over to her, holding her shoulder to prevent her from flopping onto her side as she struggled to get out of her chair. She kicked her feet and pulled at her bonds. The man took her chin in one hand, the other holding onto the chair to steady her, "Calm, calm, calm down," he said looking into her eyes. He was completely unfazed by the death. "I suppose that is a bit disturbing. You knew him didn't you."

Molly was breathing very heavily now. Her eyes were wide as she stared into the man's face. He shushed her like a child before reaching into his coat to pull out a red cloth bag. "I know. It's disturbing looking into the face of death. I'll just cover it up shall I?"

The Engineer walked over to the body of the man. He lifted the shoulders a bit as he covered the head with the red bag so that the face was entirely obscured. Then he returned to kneel at her side. "See, nothing to it. You can't see anything now." He stroked her head once before rising to his feet and going back to adjust his '_stage_'.

Molly looked over at the body hooded in red. Only hours ago, it had been a man. He had liked cashews and jelly babies. Would she be next? Would she end up lying dead in a deserted building with a red bag over her head. When she looked back at the man, she was unable to keep the fear off of her face. She began to shiver.

The engineer stood straight with his hands on his hips and smiled. He was finally happy with his setting. He had set up a table with a single chair. The back of the chair faced the door. He was sitting six feet away from the table beside the window. Molly was sitting on his right between him and the table. He pulled out a gun and aimed it at her heart. She froze, staring at the black tube on the end that she suspected was a silencer. It didn't make a difference. No one had heard her scream. No one would hear the bullet.

The man looked over at Molly's expression and shook his head "Oh don't worry dear," he said, "I don't want you dead, and I doubt that he'll try anything if you are in danger of getting hurt. Isn't that right, Mr Holmes?"

Molly whipped her head around and looked into the darkness. Near the doorway was a shadowy figure in a long coat. She looked from one man to the other. That was definitely Sherlock. How had she confused them before?

Sherlock walked slowly toward them. She could clearly see his face when he entered the circle of lamp light. She realized then what the man had been doing. He was making a place for them to talk. Sherlock stood behind the table, his hands behind his back. "I'm here. Who might you be?"

"Why, Mr. Holmes," he said, "I am glad to see you again."

"I'm sorry, have we met?"

"Not officially, although I was present at your meeting with Moriarty."

Sherlock's eyebrows raised at the mention of the name. "At the pool? You were on the balcony?"

"Yes, I was one of the little red dots. I pointed my gun straight at your forehead," he said motioning with the gun, before he turned it aside to point at Molly's heart. "So believe me when I say that I am a very good shot, and she is much closer to me now than you were then."

Sherlock glanced at Molly. "You still haven't told me who you are?"

"They call me, The Engineer."

"Ah!" Sherlock said nodding.

"So you've heard of me. I'm honored. Please take a seat, we have many things to discuss."

"I prefer to stand," Sherlock said.

"Suit yourself," he said crossing his legs, his gun always pointing toward Molly.

"I take it that you want revenge?" Sherlock said.

The man smiled at that. "Nothing so simple. That was more James' gig. You must know by now that Moriarty is more than just _one man_."

"He looked like _one man_ to me, when I saw his dead body."

The Engineer frowned, "Ah yes, that. Strange choice of retirement plan, but then again, James Moriarty always was one for the unique answer. That's what made him so valuable, his creativity."

"What did you mean when you said that he wasn't a man."

"I said that Moriarty wasn't _one_ man. Moriarty is an organization. He designed it to survive long after his death. It was to be his legacy."

"And is that why you are here, to preserve his legacy?"

"No. Are you sure that you won't sit down? My neck is getting tired."

Sherlock stared at him for a moment, and then he sat down in the chair. The Engineer placed his hand on his lap then turning a bit so that the gun still pointed at Molly. "Thank you," he said. "Moriarty was the brains of the organization. All of this was his idea. I think that he started it as a lark really. Just a bit of fun, but he was good at his job and it grew to something bigger than himself."

Sherlock smiled, "I find it funny thinking of Moriarty as a Manager in an office."

"His management style was a bit simplistic," the man said. "It was all carrot and stick with him. Oh you remember. 'I_'ll make you rich_' or '_I'll turn you into shoes_', and that temper!" he shook his head. "Even so, his methods were effective. We made quite a bit of money before his infatuation got in the way."

"By infatuation, I suppose that you mean me," Sherlock said.

"Yes," he said, "but we accepted his... eccentricities because he made us very, very rich."

"So what is this about if not revenge?"

The Engineer sat back in his chair and smiled, "Good, thank you for taking your hand off the gun in your pocket. I appreciate that. I'll follow suit." He put the safety on the gun in his hand, and put it down on a table beside his chair. "I'm here today because I'm thinking of my own retirement."

"I can help you with that," Sherlock said glancing toward the gun.

The man laughed, "No I don't plan to go like James did. I am much more traditional. I want enough money to live comfortably, and time to pursue other hobbies."

"And how much money do you need to be comfortable?"

"I am a modest man. I think that I could be happy with...thirty million."

"Thirty million pounds? And how do you expect to get such money?" Sherlock asked. "I'm sure that you are aware that I am not a rich man."

"Good, good, you're right on track. You see after Moriarty's death, there was a bit of a problem with the chain of command. Moran is the leader now..."

"But you want to be leader, right?"

"Wrong. I leave that for others."

"I see, you are the power behind the throne."

"I prefer to think of myself as a kingmaker. "

"Then why not make Moran your king?"

"Because Moran is a moron. He's hired muscle. He may be the best shot in the Western hemisphere, but as a strategist, he is pathetic. I need someone who can think to help me run my operation so that I can raise the money that I need for my retirement."

"And what makes you think that I would help you?"

"Because I have something that you want. You see, James never liked to have to deal with the details of transactions. He left those to others. I was his second in matters of organization. I kept track of all of the little cogs and wheels that made his engine go."

"And that interests me, how?"

"You see, I know what you're after, Mr Holmes. It's really quite touching. You're not like your image at all. You wish for the power to dismantle Moriarty's organization so that your friend's lives will be safe. I've been watching you picking at the edges of it. That's how I found you. Only you had the proper motive. I realized that you must still be alive, so I followed Miss Hooper, until she led me to you."

"What do you have that I want?" Sherlock asked.

"Information. I know virtually every person in Moriarty's organization, and how they are related. I can help you bring them down."

"Why would you bring down your own organization?"

"Once I get my retirement money, I don't care what happens to the rest of them."

"But you've told me who is in charge. I can just kill Moran. Then my friends will be safe."

"It doesn't work that way," he said. "Moriarty was not a trusting man. Even after death he has his ways of making people do what he wants. His standing orders say that you were to jump to your death, and if you did not die, then your friends were to be killed immediately. Do you honestly believe that he couldn't find a way to guarantee that his will would be carried out in your case? He died for you. Of course he meant to torment you throughout eternity. Even if you destroy ninety percent of his organization, the last ten percent would make sure that his will was done. No, without me, you will never be able to save your friends."

"I still don't understand what you want," Sherlock said.

"I want you to work for me."

"Doing what?"

"Since Moriarty's death, the town is full of riffraff trying to take over his operations. They've been cutting into my profit margin. I want to find their weaknesses and close them down. Actually, you'd be doing what you always do, fighting crime. You can't object to that."

Sherlock rose to his feet then. "And yet, I'm not convinced. I think that I'll just have to do the best I can alone." The Engineer picked up his gun, but before he could even turn it toward Molly again, there was a loud crack. Molly looked up to see the roof was starting to cave in.

Sherlock jumped forward grabbing Molly's chair and covering her as wood and plaster fell to the floor crushing the table and overturning the lamps so that the room was filled with darkness.

The air was full of dust. Molly felt something heavy on her legs. A beam of wood was pressed against her ankle and she couldn't stand. Sherlock's deep voice said "Molly, let's get out of here." His hands reached under her armpits and dragged her across the floor out of the rubble, then he reached down and began cutting her bonds until she was freed. He helped her to her feet.

The room was still full of dust, but Molly was beginning to be able to see from the light seeping in through the windows. She leaned against Sherlock and hobbled with him toward the door. If they could reach her car, they would be alright._ 'Are my keys still in her pocket?' _she wondered.

Just then Molly slipped on a piece of plaster and fell to the floor pulling Sherlock down with her. He climbed up on his knee and reached an arm around her waist. "Come on Molly, just a bit further," he said as he half-dragged her toward the door. He pushed it open and then froze at the clicking sound of a safety being removed from a pistol. The pistol that The Engineer was aiming directly at his temple.

"Good try, Mr Holmes, but I'm afraid that I'm going to have to insist that you come with me."

Sherlock readied himself to leap toward the man, but he read his intentions. Taking two steps back, the Engineer lowered the gun and shot Sherlock in his left thigh. Sherlock fell to the ground. "The next bullet, Mr Holmes, goes into her brain."

Molly knelt frozen in fear. Sherlock gritted his teeth clasping his hands over the wound in his leg, before sighing in defeat. They were well and truly caught.


End file.
